Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: NNQRQ

Calculation Name: 4JG2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JG2

Chain ID: A

ChEMBL ID:

UniProt ID: Q73EI2

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1814801.334389
FMO2-HF: Nuclear repulsion 1744860.447583
FMO2-HF: Total energy -69940.886806
FMO2-MP2: Total energy -70148.124635


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:-11:LYS)


Summations of interaction energy for fragment #1(A:-11:LYS)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-106.366-102.92153.555-27.945-29.058-0.226
Interaction energy analysis for fragmet #1(A:-11:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.861 / q_NPA : 0.908
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A-9THR00.001-0.0063.8783.7726.125-0.015-1.201-1.1380.004
4A-8GLU-1-0.771-0.8211.642-143.703-147.16128.107-13.707-10.942-0.148
5A-7ASN00.0380.0144.4273.8153.957-0.001-0.017-0.1240.000
6A-6LEU00.0580.0184.932-1.993-1.9930.0000.0000.0000.000
7A-5TYR0-0.0100.0056.3470.2810.2810.0000.0000.0000.000
8A-4PHE0-0.051-0.0337.2091.5161.5160.0000.0000.0000.000
9A-3GLN0-0.066-0.0172.395-5.695-4.7691.009-0.705-1.2310.001
10A-2SER0-0.012-0.0331.808-19.893-20.90312.960-6.159-5.791-0.062
11A-1ASN0-0.011-0.0054.1623.1263.6490.000-0.180-0.343-0.001
12A0ALA00.0120.0144.8925.4035.4030.0000.0000.0000.000
13A4GLN00.0290.0052.252-23.929-20.3659.231-5.791-7.004-0.019
14A5ASN0-0.017-0.0132.2473.9884.3672.253-0.349-2.283-0.001
15A6ARG10.8730.9223.52524.24324.2690.0110.164-0.2020.000
16A7THR00.0290.0106.9321.7731.7730.0000.0000.0000.000
17A8LYS10.9160.9705.46940.51340.5130.0000.0000.0000.000
18A9VAL00.0060.0076.903-0.287-0.2870.0000.0000.0000.000
19A10VAL0-0.025-0.0217.961-0.242-0.2420.0000.0000.0000.000
20A11THR00.0420.02010.5240.0610.0610.0000.0000.0000.000
21A12SER00.0340.00013.928-0.268-0.2680.0000.0000.0000.000
22A13VAL00.003-0.00615.6600.2170.2170.0000.0000.0000.000
23A14ASN0-0.0030.01018.1220.9070.9070.0000.0000.0000.000
24A15THR0-0.0070.01217.6230.3510.3510.0000.0000.0000.000
25A16ARG10.8500.92820.21310.41910.4190.0000.0000.0000.000
26A17LEU0-0.0140.00220.474-0.362-0.3620.0000.0000.0000.000
27A18SER00.0960.03623.9600.6740.6740.0000.0000.0000.000
28A19TYR0-0.071-0.04825.937-0.438-0.4380.0000.0000.0000.000
29A20PHE0-0.017-0.01122.132-0.404-0.4040.0000.0000.0000.000
30A21HIS00.0220.01624.6450.4730.4730.0000.0000.0000.000
31A22GLY00.0440.01322.094-0.430-0.4300.0000.0000.0000.000
32A23TRP00.000-0.02122.440-0.582-0.5820.0000.0000.0000.000
33A24GLU-1-0.826-0.89025.036-10.348-10.3480.0000.0000.0000.000
34A25PRO0-0.070-0.01624.762-0.182-0.1820.0000.0000.0000.000
35A26VAL00.0840.03326.2290.3550.3550.0000.0000.0000.000
36A27SER00.003-0.00127.953-0.282-0.2820.0000.0000.0000.000
37A28ILE0-0.011-0.01426.6820.0460.0460.0000.0000.0000.000
38A29ASN0-0.036-0.02730.651-0.152-0.1520.0000.0000.0000.000
39A30GLY00.0860.05833.6250.1400.1400.0000.0000.0000.000
40A31GLY0-0.037-0.00829.946-0.043-0.0430.0000.0000.0000.000
41A32ALA0-0.023-0.02227.179-0.032-0.0320.0000.0000.0000.000
42A33GLU-1-0.897-0.94127.116-10.795-10.7950.0000.0000.0000.000
43A34LYS10.8030.89022.06511.75711.7570.0000.0000.0000.000
44A35TYR00.1010.07220.6710.2920.2920.0000.0000.0000.000
45A36SER0-0.055-0.05521.476-0.285-0.2850.0000.0000.0000.000
46A37VAL00.0300.00920.3990.1460.1460.0000.0000.0000.000
47A38SER0-0.038-0.00821.926-0.368-0.3680.0000.0000.0000.000
48A39VAL0-0.021-0.00917.7080.2160.2160.0000.0000.0000.000
49A40LEU00.0290.01521.078-0.040-0.0400.0000.0000.0000.000
50A41ILE0-0.012-0.01717.236-0.410-0.4100.0000.0000.0000.000
51A42PRO00.0630.03720.8440.3170.3170.0000.0000.0000.000
52A43LYS10.8070.87721.9079.8139.8130.0000.0000.0000.000
53A44THR0-0.006-0.00822.995-0.067-0.0670.0000.0000.0000.000
54A45ASP-1-0.777-0.83416.733-15.778-15.7780.0000.0000.0000.000
55A46LYS10.9150.92317.86811.36211.3620.0000.0000.0000.000
56A47GLU-1-0.935-0.94412.205-18.538-18.5380.0000.0000.0000.000
57A48THR00.011-0.02113.379-1.288-1.2880.0000.0000.0000.000
58A49ILE0-0.017-0.00814.324-0.479-0.4790.0000.0000.0000.000
59A50ASN0-0.009-0.00314.7170.3680.3680.0000.0000.0000.000
60A51ALA00.0070.01510.112-0.330-0.3300.0000.0000.0000.000
61A52ILE00.0150.00311.705-0.750-0.7500.0000.0000.0000.000
62A53ASN0-0.054-0.03413.8360.3510.3510.0000.0000.0000.000
63A54ALA00.0110.00911.7250.1720.1720.0000.0000.0000.000
64A55ALA00.0260.02110.315-0.316-0.3160.0000.0000.0000.000
65A56VAL0-0.043-0.02611.8080.0610.0610.0000.0000.0000.000
66A57ASP-1-0.830-0.91115.414-14.222-14.2220.0000.0000.0000.000
67A58ALA0-0.021-0.00110.8630.3380.3380.0000.0000.0000.000
68A59ALA00.0250.01812.955-0.017-0.0170.0000.0000.0000.000
69A60ILE0-0.054-0.02913.9690.6950.6950.0000.0000.0000.000
70A61GLU-1-0.802-0.87214.869-16.625-16.6250.0000.0000.0000.000
71A62GLU-1-0.855-0.94110.098-25.381-25.3810.0000.0000.0000.000
72A63GLY0-0.0050.00114.4970.2220.2220.0000.0000.0000.000
73A64ILE0-0.056-0.03117.6300.5220.5220.0000.0000.0000.000
74A65ALA0-0.015-0.00815.5860.4970.4970.0000.0000.0000.000
75A66LYS10.9060.97616.21116.12516.1250.0000.0000.0000.000
76A67PHE0-0.046-0.03917.9790.3350.3350.0000.0000.0000.000
77A68GLY00.0380.04221.4150.6490.6490.0000.0000.0000.000
78A69GLY0-0.001-0.00523.372-0.021-0.0210.0000.0000.0000.000
79A70LYS10.9520.97124.7269.5219.5210.0000.0000.0000.000
80A71LYS10.9130.93118.72614.35714.3570.0000.0000.0000.000
81A72PRO0-0.021-0.00122.1980.5000.5000.0000.0000.0000.000
82A73ASN00.0390.01124.455-0.455-0.4550.0000.0000.0000.000
83A74LYS10.9070.91919.59913.84413.8440.0000.0000.0000.000
84A75ALA00.0320.02524.839-0.085-0.0850.0000.0000.0000.000
85A76ALA0-0.042-0.01227.6930.3110.3110.0000.0000.0000.000
86A77ILE0-0.073-0.04422.210-0.009-0.0090.0000.0000.0000.000
87A78LYS10.9240.96024.00711.14011.1400.0000.0000.0000.000
88A79LEU00.0380.01020.826-0.566-0.5660.0000.0000.0000.000
89A80PRO0-0.0080.00317.6100.5050.5050.0000.0000.0000.000
90A81LEU0-0.011-0.00318.5840.0690.0690.0000.0000.0000.000
91A82ARG10.7600.86020.87411.70611.7060.0000.0000.0000.000
92A83ASP-1-0.781-0.89224.358-10.513-10.5130.0000.0000.0000.000
93A84GLY00.004-0.01126.7410.2550.2550.0000.0000.0000.000
94A85ASP-1-0.758-0.85828.339-9.315-9.3150.0000.0000.0000.000
95A86VAL0-0.023-0.01330.6000.2980.2980.0000.0000.0000.000
96A87GLU-1-0.829-0.87427.633-10.564-10.5640.0000.0000.0000.000
97A88ARG10.8350.91529.1259.8709.8700.0000.0000.0000.000
98A89ASP-1-0.791-0.88732.491-8.180-8.1800.0000.0000.0000.000
99A90ASP-1-0.854-0.90731.881-9.067-9.0670.0000.0000.0000.000
100A91GLU-1-0.852-0.94532.631-8.491-8.4910.0000.0000.0000.000
101A92ALA0-0.081-0.03529.925-0.134-0.1340.0000.0000.0000.000
102A93TYR0-0.065-0.04426.918-0.562-0.5620.0000.0000.0000.000
103A94LYS10.8870.94728.6138.3948.3940.0000.0000.0000.000
104A95GLY00.0070.00928.924-0.147-0.1470.0000.0000.0000.000
105A96HIS0-0.091-0.05924.050-0.681-0.6810.0000.0000.0000.000
106A97TYR0-0.0030.00321.5750.1860.1860.0000.0000.0000.000
107A98PHE0-0.010-0.01321.879-0.176-0.1760.0000.0000.0000.000
108A99VAL00.0190.01217.194-0.145-0.1450.0000.0000.0000.000
109A100ASN0-0.020-0.00320.5680.1520.1520.0000.0000.0000.000
110A101ALA00.0280.02717.529-0.138-0.1380.0000.0000.0000.000
111A102ASN0-0.040-0.03718.6880.7670.7670.0000.0000.0000.000
112A103SER00.0360.02016.293-0.694-0.6940.0000.0000.0000.000
113A104LYS10.9530.97418.88713.20313.2030.0000.0000.0000.000
114A105THR00.0020.01916.8240.4340.4340.0000.0000.0000.000
115A106PRO00.0210.01918.687-0.320-0.3200.0000.0000.0000.000
116A107PRO0-0.0420.00116.044-0.977-0.9770.0000.0000.0000.000
117A108GLN00.0370.00613.189-0.620-0.6200.0000.0000.0000.000
118A109ILE0-0.0130.00916.461-0.746-0.7460.0000.0000.0000.000
119A110VAL00.0000.00015.5350.3550.3550.0000.0000.0000.000
120A111ASP-1-0.694-0.83718.933-14.228-14.2280.0000.0000.0000.000
121A112LYS10.8860.93218.48812.37412.3740.0000.0000.0000.000
122A113ALA0-0.050-0.01118.745-0.320-0.3200.0000.0000.0000.000
123A114VAL0-0.042-0.02413.440-0.574-0.5740.0000.0000.0000.000
124A115ARG10.8970.93516.79112.88212.8820.0000.0000.0000.000
125A116PRO0-0.001-0.01519.1550.0870.0870.0000.0000.0000.000
126A117ILE0-0.0270.00020.9320.5410.5410.0000.0000.0000.000
127A118LEU0-0.027-0.01923.700-0.047-0.0470.0000.0000.0000.000
128A119ASP-1-0.801-0.88926.897-9.641-9.6410.0000.0000.0000.000
129A120ARG10.8500.88627.57410.35510.3550.0000.0000.0000.000
130A121ASN0-0.047-0.04028.568-0.056-0.0560.0000.0000.0000.000
131A122GLU-1-0.865-0.90825.933-11.268-11.2680.0000.0000.0000.000
132A123VAL0-0.050-0.03222.559-0.344-0.3440.0000.0000.0000.000
133A124TYR00.012-0.02325.7970.1210.1210.0000.0000.0000.000
134A125SER00.0220.00327.035-0.489-0.4890.0000.0000.0000.000
135A126GLY00.0670.04727.4060.4330.4330.0000.0000.0000.000
136A127CYS0-0.0680.01625.047-0.182-0.1820.0000.0000.0000.000
137A128TYR00.042-0.00623.034-0.073-0.0730.0000.0000.0000.000
138A129ALA00.0490.00819.883-0.036-0.0360.0000.0000.0000.000
139A130ARG10.8290.92310.92020.72620.7260.0000.0000.0000.000
140A131VAL00.0480.01615.2930.0090.0090.0000.0000.0000.000
141A132SER0-0.025-0.01510.081-2.021-2.0210.0000.0000.0000.000
142A133LEU0-0.027-0.01411.1381.2581.2580.0000.0000.0000.000
143A134ASN00.0260.0188.365-4.787-4.7870.0000.0000.0000.000
144A135PHE00.0180.00610.9311.9461.9460.0000.0000.0000.000
145A136TYR00.006-0.00912.114-0.985-0.9850.0000.0000.0000.000
146A137ALA00.0440.02414.6811.0171.0170.0000.0000.0000.000
147A138PHE0-0.054-0.02517.834-0.103-0.1030.0000.0000.0000.000
148A139ASN00.011-0.01820.9150.5750.5750.0000.0000.0000.000
149A140SER00.0130.02224.686-0.053-0.0530.0000.0000.0000.000
150A141ASN00.0310.00526.7860.3070.3070.0000.0000.0000.000
151A142GLY00.0580.04129.8340.1120.1120.0000.0000.0000.000
152A143ASN0-0.055-0.01726.6520.0040.0040.0000.0000.0000.000
153A144LYS10.9960.99824.80310.01210.0120.0000.0000.0000.000
154A145GLY00.0100.01322.4800.3540.3540.0000.0000.0000.000
155A146VAL0-0.037-0.00916.418-0.450-0.4500.0000.0000.0000.000
156A147ALA0-0.0140.00217.9220.6750.6750.0000.0000.0000.000
157A148CYS0-0.019-0.02115.384-0.883-0.8830.0000.0000.0000.000
158A149GLY00.0310.02514.4870.8270.8270.0000.0000.0000.000
159A150LEU0-0.023-0.01613.972-1.183-1.1830.0000.0000.0000.000
160A151GLY00.0160.00512.369-0.460-0.4600.0000.0000.0000.000
161A152ASN0-0.033-0.03512.0491.7461.7460.0000.0000.0000.000
162A153ILE00.0200.01514.161-0.397-0.3970.0000.0000.0000.000
163A154GLN0-0.046-0.02715.520-0.391-0.3910.0000.0000.0000.000
164A155LYS10.8040.89017.53911.81711.8170.0000.0000.0000.000
165A156ILE0-0.095-0.04417.532-0.213-0.2130.0000.0000.0000.000
166A157ARG10.8740.93121.62011.98611.9860.0000.0000.0000.000
167A158ASP-1-0.741-0.84425.285-11.117-11.1170.0000.0000.0000.000
168A159GLY0-0.034-0.02728.374-0.094-0.0940.0000.0000.0000.000
169A160GLU-1-0.892-0.93130.153-8.700-8.7000.0000.0000.0000.000
170A161PRO00.0120.00331.654-0.296-0.2960.0000.0000.0000.000
171A162LEU0-0.043-0.02028.7070.1690.1690.0000.0000.0000.000
172A163GLY00.0240.01132.577-0.058-0.0580.0000.0000.0000.000
173A164GLY00.0040.00332.703-0.330-0.3300.0000.0000.0000.000
174A165ARG10.9090.94827.10410.80310.8030.0000.0000.0000.000
175A166THR00.0120.00734.414-0.005-0.0050.0000.0000.0000.000
176A167ASN0-0.092-0.06835.1940.1440.1440.0000.0000.0000.000
177A168ALA00.0580.04037.3410.0110.0110.0000.0000.0000.000
178A169ALA0-0.013-0.00840.3090.1340.1340.0000.0000.0000.000
179A170ASP-1-0.900-0.93935.801-8.580-8.5800.0000.0000.0000.000
180A171ASP-1-0.967-0.97038.484-8.236-8.2360.0000.0000.0000.000
181A172PHE0-0.082-0.04340.7820.1700.1700.0000.0000.0000.000
182A173THR0-0.009-0.00644.446-0.059-0.0590.0000.0000.0000.000
183A174THR0-0.044-0.05346.953-0.024-0.0240.0000.0000.0000.000
184A175ILE0-0.027-0.00750.008-0.007-0.0070.0000.0000.0000.000
185A176GLU-1-0.912-0.92352.799-5.889-5.8890.0000.0000.0000.000